Input and runtime details for job 3202356 (precomputed example)

Sequence input

	sRNA sequences		[.fa]
	Putative target sequences (organism of interest)		[.fa]
	Extract sequences around		start codon
	nt up (1-300)		200
	nt down (1-300)		100

CopraRNA parameters

	Consensus prediction		off
	p-value combination		no
	p-value filtering (0=off)		0

IntaRNA parameters

	Target folding window size		150
	Target max. basepair distance		100

Job ID 3202356 (server version trunk)

	Job Submitted & Queued		@ Fri Feb 16 15:24:02 CET 2018
	CopraRNA Started		@ Fri Feb 16 15:24:35 CET 2018
	CopraRNA Finished & Post-Processing		@ Sat Feb 17 02:03:47 CET 2018
	Post-Processing Finished		@ Sat Feb 17 02:03:55 CET 2018
	Job Completed		@ Sat Feb 17 02:04:28 CET 2018

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

Output download complete results [zip]

Downloadable files

	CopraRNA result table:		[csv]
	Functional enrichment file		[txt]
	Auxiliary enrichment file		[csv]
	mRNA regions plot		[png] [pdf] [ps]
	sRNA regions plot		[png] [pdf] [ps]
	Functional annotation chart		[html] [pdf]
	Phylogenetic conservation		[png] [pdf]
	16S rDNA tree		[txt] [svg]

mRNA region plot

sRNA region plot

Annot. chart

Conserved, identified interactions for NC_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

Select: 1-10 11-20 21-30 31-40 41-50 51-60 61-70 71-80 81-90 91-100 101-110 111-120 121-130 131-140 141-150 151-160 161-170 171-180 181-190 191-200 all

Sort by selecting a column name:

Rank	CopraRNA p-value	CopraRNA fdr value	Locus Tag	Gene Name	Energy [kcal/mol]	IntaRNA p-value	Position mRNA	Position sRNA	Annotation	Additional homologs
142	0.007269	0.182	stm4341	frdC	-12.15	0.319206	131 -- 234	54 -- 160	fumarate reductase subunit C		_____________130__________________235\n_____________\|____________________\|\n5'-AGA...AGGAG_______________UA___GCAAA...CGG-3'\n______________UGC_AACAUGACGAC__AAC\n______________\|\|\|_\|\|\|\|::\|\|:\|\|__\|\|\|\n______________ACG_UUGUGUUGUUG__UUG\n3'-UUU...GGUUA___U___________UG___UAGUG...UCA-5'\n_____________\|____________________\|\n_____________161__________________53\n	202 -- 208	77 -- 83	-18.8897 kcal/mol	4.02107 kcal/mol	3.80548 kcal/mol	130 235@LB@ \| \|@LB@5'-AGA...AGGAG UA GCAAA...CGG-3'@LB@ UGC AACAUGACGAC AAC@LB@ \|\|\| \|\|\|\|::\|\|:\|\| \|\|\|@LB@ ACG UUGUGUUGUUG UUG@LB@3'-UUU...GGUUA U UG UAGUG...UCA-5'@LB@ \| \|@LB@ 161 53@LB@@LB@@LB@Energy -12.15 kcal/mol@LB@Hybridization Energy -18.8897 kcal/mol@LB@Unfolding Energy - mRNA 4.02107 kcal/mol@LB@Unfolding Energy - sRNA 3.80548 kcal/mol@LB@@LB@Position - mRNA 131 -- 234@LB@Position - sRNA 54 -- 160@LB@Position Seed - mRNA 202 -- 208@LB@Position Seed - sRNA 77 -- 83@LB@
109	0.005328	0.1728	stm3082	N/A	-12.60	0.275269	106 -- 154	38 -- 90	galactonate oxidoreductase		_____________105________________________155\n_____________\|__________________________\|\n5'-AAU...ACAAC______UUUUUA_______UU_____GGCCU...CGG-3'\n______________GCAGAC______AACAACA__CAGCA\n______________\|\|\|:\|\|______\|\|\|\|\|\|\|__\|\|:\|\|\n______________CGUUUG______UUGUUGU__GUUGU\n3'-UUU...GUUAA______UG__________________AGUGU...UCA-5'\n_____________\|__________________________\|\n_____________91_________________________37\n	118 -- 124	76 -- 82	-16.9817 kcal/mol	2.50135 kcal/mol	3.80671 kcal/mol	105 155@LB@ \| \|@LB@5'-AAU...ACAAC UUUUUA UU GGCCU...CGG-3'@LB@ GCAGAC AACAACA CAGCA@LB@ \|\|\|:\|\| \|\|\|\|\|\|\| \|\|:\|\|@LB@ CGUUUG UUGUUGU GUUGU@LB@3'-UUU...GUUAA UG AGUGU...UCA-5'@LB@ \| \|@LB@ 91 37@LB@@LB@@LB@Energy -12.60 kcal/mol@LB@Hybridization Energy -16.9817 kcal/mol@LB@Unfolding Energy - mRNA 2.50135 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 106 -- 154@LB@Position - sRNA 38 -- 90@LB@Position Seed - mRNA 118 -- 124@LB@Position Seed - sRNA 76 -- 82@LB@
135	0.006796	0.1774	stm1044	sodC	-14.39	0.147293	208 -- 244	43 -- 78	Gifsy-2 prophage superoxide dismutase precursor (Cu-Zn)	stm1440 stm0924	_____________207__________245\n_____________\|____________\|\n5'-GAA...GCUUU____________CAGGG...CCA-3'\n______________GGUGGUCUCGCU\n______________\|\|\|:\|\|\|\|\|\|\|\|\n______________CCAUCAGAGCGA\n3'-UUU...UUUUC____________UGGCA...UCA-5'\n_____________\|____________\|\n_____________79___________42\n	78 -- 84	117 -- 123	-21.9622 kcal/mol	4.44224 kcal/mol	6.55795 kcal/mol	207 245@LB@ \| \|@LB@5'-GAA...GCUUU CAGGG...CCA-3'@LB@ GGUGGUCUCGCU@LB@ \|\|\|:\|\|\|\|\|\|\|\|@LB@ CCAUCAGAGCGA@LB@3'-UUU...UUUUC UGGCA...UCA-5'@LB@ \| \|@LB@ 79 42@LB@@LB@@LB@Energy -14.39 kcal/mol@LB@Hybridization Energy -21.9622 kcal/mol@LB@Unfolding Energy - mRNA 4.44224 kcal/mol@LB@Unfolding Energy - sRNA 6.55795 kcal/mol@LB@@LB@Position - mRNA 208 -- 244@LB@Position - sRNA 43 -- 78@LB@Position Seed - mRNA 78 -- 84@LB@Position Seed - sRNA 117 -- 123@LB@
162	0.00849	0.1864	stm4221	pgi	-15.16	0.111294	249 -- 289	56 -- 88	glucose-6-phosphate isomerase		_____________248_______________________________________290\n_____________\|_________________________________________\|\n5'-GCU...UCCAG______U_____GAAAUGAAA_____________C______UUUCG...ACG-3'\n______________AAACAC_ACGAU_________GACGUUACGAUCG_UGAGCU\n______________\|\|\|\|\|\|_\|\|:\|:_________:\|\|:\|:\|\|:\|:\|\|_\|:\|\|\|:\n______________UUUGUG_UGUUG_________UUGUAGUGUUGGC_AUUCGG\n3'-UUU...UAACG______U_____UG___________________________UUUUC...UCA-5'\n_____________\|_________________________________________\|\n_____________89________________________________________55\n	272 -- 278	66 -- 72	-30.3131 kcal/mol	6.22888 kcal/mol	11.698 kcal/mol	248 290@LB@ \| \|@LB@5'-GCU...UCCAG U GAAAUGAAA C UUUCG...ACG-3'@LB@ AAACAC ACGAU GACGUUACGAUCG UGAGCU@LB@ \|\|\|\|\|\| \|\|:\|: :\|\|:\|:\|\|:\|:\|\| \|:\|\|\|:@LB@ UUUGUG UGUUG UUGUAGUGUUGGC AUUCGG@LB@3'-UUU...UAACG U UG UUUUC...UCA-5'@LB@ \| \|@LB@ 89 55@LB@@LB@@LB@Energy -15.16 kcal/mol@LB@Hybridization Energy -30.3131 kcal/mol@LB@Unfolding Energy - mRNA 6.22888 kcal/mol@LB@Unfolding Energy - sRNA 11.698 kcal/mol@LB@@LB@Position - mRNA 249 -- 289@LB@Position - sRNA 56 -- 88@LB@Position Seed - mRNA 272 -- 278@LB@Position Seed - sRNA 66 -- 72@LB@
62	0.003015	0.1596	stm1299	gdhA	-15.31	0.105026	136 -- 171	63 -- 91	glutamate dehydrogenase		_____________135____________________________________172\n_____________\|______________________________________\|\n5'-CGG...AAAAC__________UAUUCUGAUAA_______A_________ACAUU...CCA-3'\n______________UGCAAAUACA___________AACGCAA___UACAACC\n______________\|\|\|\|\|\|:\|\|\|___________\|\|\|:\|\|\|___:\|\|\|\|\|\|\n______________ACGUUUGUGU___________UUGUGUU___GUGUUGG\n3'-UUU...GGUUA__________UG________________GUA_______CAUUC...UCA-5'\n_____________\|______________________________________\|\n_____________92_____________________________________62\n	165 -- 171	63 -- 69	-26.3361 kcal/mol	2.66287 kcal/mol	8.61685 kcal/mol	135 172@LB@ \| \|@LB@5'-CGG...AAAAC UAUUCUGAUAA A ACAUU...CCA-3'@LB@ UGCAAAUACA AACGCAA UACAACC@LB@ \|\|\|\|\|\|:\|\|\| \|\|\|:\|\|\| :\|\|\|\|\|\|@LB@ ACGUUUGUGU UUGUGUU GUGUUGG@LB@3'-UUU...GGUUA UG GUA CAUUC...UCA-5'@LB@ \| \|@LB@ 92 62@LB@@LB@@LB@Energy -15.31 kcal/mol@LB@Hybridization Energy -26.3361 kcal/mol@LB@Unfolding Energy - mRNA 2.66287 kcal/mol@LB@Unfolding Energy - sRNA 8.61685 kcal/mol@LB@@LB@Position - mRNA 136 -- 171@LB@Position - sRNA 63 -- 91@LB@Position Seed - mRNA 165 -- 171@LB@Position Seed - sRNA 63 -- 69@LB@
6	7.515e-05	0.04123	stm0665	gltI	-17.87	0.039793	157 -- 199	35 -- 81	glutamate/aspartate transporter		_____________156__________________200\n_____________\|____________________\|\n5'-CGA...UGCAG____UA______U_______GCUAU...CUG-3'\n______________GCAA__ACAACA_CACAAUA\n______________\|\|\|\|__\|\|\|\|\|\|_\|\|\|\|\|:\|\n______________CGUU__UGUUGU_GUGUUGU\n3'-UUU...GUUAA____UG______U_______AGUGU...UCA-5'\n_____________\|____________________\|\n_____________82___________________34\n	170 -- 176	71 -- 77	-19.9204 kcal/mol	1.29616 kcal/mol	3.80671 kcal/mol	156 200@LB@ \| \|@LB@5'-CGA...UGCAG UA U GCUAU...CUG-3'@LB@ GCAA ACAACA CACAAUA@LB@ \|\|\|\| \|\|\|\|\|\| \|\|\|\|\|:\|@LB@ CGUU UGUUGU GUGUUGU@LB@3'-UUU...GUUAA UG U AGUGU...UCA-5'@LB@ \| \|@LB@ 82 34@LB@@LB@@LB@Energy -17.87 kcal/mol@LB@Hybridization Energy -19.9204 kcal/mol@LB@Unfolding Energy - mRNA 1.29616 kcal/mol@LB@Unfolding Energy - sRNA 3.80671 kcal/mol@LB@@LB@Position - mRNA 157 -- 199@LB@Position - sRNA 35 -- 81@LB@Position Seed - mRNA 170 -- 176@LB@Position Seed - sRNA 71 -- 77@LB@
65	0.003171	0.1596	stm0830	glnH	-11.06	0.446113	180 -- 193	153 -- 165	glutamine ABC transporter substrate-binding protein GlnH		_____________179____________194\n_____________\|______________\|\n5'-AGA...GCCCC_________AA___AAAUG...CGG-3'\n______________GUGGAUAGA__AGG\n______________:\|\|\|\|:\|\|\|__\|\|\|\n______________UACCUGUCU__UCC\n3'-UUU...AGUGA_________G____CAUUU...UCA-5'\n_____________\|______________\|\n_____________166____________152\n	182 -- 188	157 -- 163	-15.2236 kcal/mol	3.11192 kcal/mol	2.82582 kcal/mol	179 194@LB@ \| \|@LB@5'-AGA...GCCCC AA AAAUG...CGG-3'@LB@ GUGGAUAGA AGG@LB@ :\|\|\|\|:\|\|\| \|\|\|@LB@ UACCUGUCU UCC@LB@3'-UUU...AGUGA G CAUUU...UCA-5'@LB@ \| \|@LB@ 166 152@LB@@LB@@LB@Energy -11.06 kcal/mol@LB@Hybridization Energy -15.2236 kcal/mol@LB@Unfolding Energy - mRNA 3.11192 kcal/mol@LB@Unfolding Energy - sRNA 2.82582 kcal/mol@LB@@LB@Position - mRNA 180 -- 193@LB@Position - sRNA 153 -- 165@LB@Position Seed - mRNA 182 -- 188@LB@Position Seed - sRNA 157 -- 163@LB@
72	0.003348	0.1596	stm0849	yliB	-19.23	0.023527	175 -- 193	139 -- 162	glutathione ABC transporter substrate-binding protein GsiB		_____________174______________________194\n_____________\|________________________\|\n5'-GUU...AUUCA____________UU__________GAACA...CGG-3'\n______________GACAGGCAGGGU_______CAGGA\n______________\|\|\|\|\|:\|\|\|\|\|\|_______\|\|\|\|\|\n______________CUGUCUGUCCCA_______GUCCU\n3'-UUU...GAUAC____________UUUACAU_____UCACU...UCA-5'\n_____________\|________________________\|\n_____________163______________________138\n	180 -- 186	151 -- 157	-27.2027 kcal/mol	3.52422 kcal/mol	3.69132 kcal/mol	174 194@LB@ \| \|@LB@5'-GUU...AUUCA UU GAACA...CGG-3'@LB@ GACAGGCAGGGU CAGGA@LB@ \|\|\|\|\|:\|\|\|\|\|\| \|\|\|\|\|@LB@ CUGUCUGUCCCA GUCCU@LB@3'-UUU...GAUAC UUUACAU UCACU...UCA-5'@LB@ \| \|@LB@ 163 138@LB@@LB@@LB@Energy -19.23 kcal/mol@LB@Hybridization Energy -27.2027 kcal/mol@LB@Unfolding Energy - mRNA 3.52422 kcal/mol@LB@Unfolding Energy - sRNA 3.69132 kcal/mol@LB@@LB@Position - mRNA 175 -- 193@LB@Position - sRNA 139 -- 162@LB@Position Seed - mRNA 180 -- 186@LB@Position Seed - sRNA 151 -- 157@LB@
98	0.004857	0.1728	stm2811	proX	-15.53	0.097032	195 -- 224	56 -- 84	glycine betaine ABC transporter substrate-binding protein		_____________194________________________225\n_____________\|__________________________\|\n5'-GCA...AAGGA__________________________UAUUU...CUA-3'\n______________ACAACGAUGCGACAU____ACCGUGA\n______________\|\|\|\|\|:\|::\|:\|\|\|\|____\|\|\|\|\|:\|\n______________UGUUGUUGUGUUGUA____UGGCAUU\n3'-UUU...GUUUG_______________GUGU_______CGGUU...UCA-5'\n_____________\|__________________________\|\n_____________85_________________________55\n	210 -- 216	59 -- 65	-26.0076 kcal/mol	3.5169 kcal/mol	9.80321 kcal/mol	194 225@LB@ \| \|@LB@5'-GCA...AAGGA UAUUU...CUA-3'@LB@ ACAACGAUGCGACAU ACCGUGA@LB@ \|\|\|\|\|:\|::\|:\|\|\|\| \|\|\|\|\|:\|@LB@ UGUUGUUGUGUUGUA UGGCAUU@LB@3'-UUU...GUUUG GUGU CGGUU...UCA-5'@LB@ \| \|@LB@ 85 55@LB@@LB@@LB@Energy -15.53 kcal/mol@LB@Hybridization Energy -26.0076 kcal/mol@LB@Unfolding Energy - mRNA 3.5169 kcal/mol@LB@Unfolding Energy - sRNA 9.80321 kcal/mol@LB@@LB@Position - mRNA 195 -- 224@LB@Position - sRNA 56 -- 84@LB@Position Seed - mRNA 210 -- 216@LB@Position Seed - sRNA 59 -- 65@LB@
200	0.01112	0.198	stm2809	proV	-15.77	0.088450	57 -- 94	50 -- 85	glycine betaine/L-proline ABC transporter ATP-binding protein		_____________56______________________________________95\n_____________\|_______________________________________\|\n5'-UUC...AUCAC_____________C__________AUUCAU_________AAAUU...AAA-3'\n______________AGC_CGAUAGCAC____UCGCAAU______GCCAGAAGC\n______________\|:\|_\|:\|:\|:\|\|\|____\|\|:\|\|\|:______\|\|\|\|:\|\|\|\|\n______________UUG_GUUGUUGUG____AGUGUUG______CGGUUUUCG\n3'-UUU...AACGU___U_________UUGU_______GCAUU__________GGUAG...UCA-5'\n_____________\|_______________________________________\|\n_____________86______________________________________49\n	65 -- 71	75 -- 81	-32.303 kcal/mol	6.98444 kcal/mol	14.5427 kcal/mol	56 95@LB@ \| \|@LB@5'-UUC...AUCAC C AUUCAU AAAUU...AAA-3'@LB@ AGC CGAUAGCAC UCGCAAU GCCAGAAGC@LB@ \|:\| \|:\|:\|:\|\|\| \|\|:\|\|\|: \|\|\|\|:\|\|\|\|@LB@ UUG GUUGUUGUG AGUGUUG CGGUUUUCG@LB@3'-UUU...AACGU U UUGU GCAUU GGUAG...UCA-5'@LB@ \| \|@LB@ 86 49@LB@@LB@@LB@Energy -15.77 kcal/mol@LB@Hybridization Energy -32.303 kcal/mol@LB@Unfolding Energy - mRNA 6.98444 kcal/mol@LB@Unfolding Energy - sRNA 14.5427 kcal/mol@LB@@LB@Position - mRNA 57 -- 94@LB@Position - sRNA 50 -- 85@LB@Position Seed - mRNA 65 -- 71@LB@Position Seed - sRNA 75 -- 81@LB@

Details of Selected Interaction Download Interaction Details

mRNA

sRNA

Energy

Hybridization Energy

Unfolding Energy - mRNA

Unfolding Energy - sRNA

Position - mRNA

Position - sRNA

Position Seed - mRNA

Position Seed - sRNA

Evolutionary conservation of mRNA targets (alignment generated with Jalview)

Evolutionary conservation of sRNA (alignment generated with Jalview)

Job resubmission

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When using CopraRNA please cite :

Patrick R. Wright, Jens Georg, Martin Mann, Dragos A. Sorescu, Andreas S. Richter, Steffen Lott, Robert Kleinkauf, Wolfgang R. Hess, and Rolf Backofen
CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains
Nucleic Acids Research, 2014, 42 (W1), W119-W123.
Patrick R. Wright, Andreas S. Richter, Kai Papenfort, Martin Mann, Joerg Vogel, Wolfgang R. Hess, Rolf Backofen and Jens Georg
Comparative genomics boosts target prediction for bacterial small RNAs
Proc Natl Acad Sci USA, 2013, 110 (37), E3487-E3496.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with CopraRNA version 2.1.2

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